Release 3.1.0

[isayev]

Why now

Everything merged since 3.0.0 has been shipping under a version number that says 3.0.0. Verified against PyPI: auto3d-3.0.0 was uploaded 2026-08-04, is not yanked, and is the latest version there — so the API changes since then land on an installed base, not on nothing.

The semver departure, stated up front

3.1.0 is a minor version carrying breaking changes. Strict semver would make this a major release. A >=3.0,<4 or ~=3.0 pin will pick it up automatically.

The CHANGELOG now opens 3.1.0 with a warning block saying exactly that, naming Auto3D==3.0.0 as the pin to hold while migrating, and stating that no compatibility shims exist.

It also leads with the mitigating fact, because that decides whether most users are affected at all: the top-level API is unchanged. from Auto3D import main, smiles2mols, Auto3DOptions, calc_spe, calc_thermo, opt_geometry, create_model, ... all still resolve — the package root re-exports them lazily. Only code reaching into submodules breaks.

CHANGELOG consolidation

[Unreleased] became ## [3.1.0] - 2026-08-20, with a fresh empty [Unreleased] above it.

Seven section headings became four. Fixed, Added and Changed each appeared twice (lines 260/491, 395/483, 435/468) because two later waves appended their own sections rather than merging into the existing ones. Entries are preserved in document order within each merged section, and sections are now in Keep a Changelog's order.

The two packaging fixes are verified against a real artifact

Both were made during the layer move, and neither is covered by any test — so this build is the first thing that has ever checked either:

entry_points.txt   auto3d = Auto3D.presentation.auto3Dcli:cli
wheel payload      Auto3D/engines/models/ani2xt_no_repulsion.pt

Without them this release ships a broken auto3d command and a wheel with no ANI2xt checkpoint — with every gate green, because the suite runs from the source tree where both are fine regardless.

python -m build also confirms Version: 3.1.0, py.typed present, all six layer directories in the wheel, and 100 layered modules in the sdist. Artifacts were inspected and deleted, not committed.

publish.yml needs no change

It builds from pyproject.toml and publishes via trusted publishing, with no module path anywhere in it. That closes a gap I flagged during the layer move: it is the one workflow no CI run exercises, because it triggers only on a published release.

Not in this PR: CLAUDE.md

It is gitignored (.gitignore:135), so the file describing the project's current version and layout is local to one machine and cannot be updated here. Worth knowing before treating it as a shared record.

Verification

• 1771 passed, 1 skipped, 74 deselected, randomized order.
• ruff check and ruff format --check both clean.
• Wheel and sdist built and inspected.

Not done here

Tagging and publishing. Creating the GitHub release is what triggers publish.yml and the PyPI upload, and PyPI never accepts a version number twice. That step is deliberately left for a human.